This subproject is one of many research subprojects utilizing the resources provided by a Center grant funded by NIH/NCRR. The subproject and investigator (PI) may have received primary funding from another NIH source, and thus could be represented in other CRISP entries. The institution listed is for the Center, which is not necessarily the institution for the investigator. The complement of DNA-binding proteins and their occupancy of sites throughout the genome determine an organism's programs of gene expression, DNA replication and other chromosome-based processes. A detailed picture of factor binding on a genome-wide basis exists for Saccharomyces cerevisiae, obtained by a combination of transcriptional profiles, chromatin immunoprecipitation of more than 200 transcription factors, computational analyses and other assays. In an alternative approach, we have used digestion of chromatin by DNase I followed by high throughput DNA sequencing to identify sites of increased nuclease accessibility throughout the yeast genome. The resulting set of more than 10 million sequence reads provides both a global view of chromatin architecture as well as a gene-by-gene view of regulatory sequences protected from digestion by the presence of bound proteins. Unlike the case with results from chromatin immunoprecipitation, these gene-by-gene DNase I footprints can be used to directly identify transcription factor binding sites, and thereby infer their motifs. We found previously unknown binding sites in the genome for well-characterized factors, and observed other annotated binding sites that appear not to be protected from nuclease digestion under our conditions.